Context: Therapeutic exercise is a recommended treatment for patellofemoral pain syndrome (PFPS). However, the literature is not clear as to which muscle groups to target for this intervention. Objective: To compare the effects of strengthening exercise targeting knee extensors, hip lateral rotators and abductors, or both on pain and function in those with PFPS. Design: Randomized controlled clinical trial. Setting: University sports medicine clinic and biometrics laboratory. Patients: Twenty-four patients with PFPS. Intervention: We randomly assigned the patients to participate in strengthening exercises targeting the knee extensor (QE), hip lateral rotators and abductors (HE), or both (HQE). The patients participated in both supervised and home exercises for 4-weeks. Main Outcome Measures: We measured perceived pain and perceived function before and after intervention using the visual analogue scale (VAS) and the Lower Extremity Functional Scale (LEFS) respectively. We also obtained isokinetic torques before and after intervention. Results: The three groups were Homogenous at baseline. We observed significant improvements in perceived pain and perceived function from pre to post intervention within the groups regardless of assignment. Our study found no statistically significant differences between the three groups for perceived pain or perceived function at the end of the 4-week intervention. Improvements in perceived pain and perceived function were largely independent of changes in strength. Conclusion: In the treatment of PFPS, targeting only the hip external rotators and abductors is equally effective as targeting only the quadriceps or a combination of the two protocols. We found improvements in perceived pain and perceived function were not attributed to improvements in strength.